Chem 406: Lab 1 - Jmol and PDB Files

Mount your chemserver volume and save an alias (shortcut) for it in your 'H' drive:

From a Mac (Mac OS X)

Select “Connect to Server...” from the Finder’s “Go” menu.

Enter “smb://username@chemserver.chem.uwec.edu/username_X” in the Server Address field, where username is your University username, and click “OK”

You will be prompted for a username and password; use your University username and password.

An icon representing your username_X volume should appear on your desktop. Double-clicking on this icon will open a Finder window showing you the contents of this volume.

Creating an aliase(shortcut) for your username_X volume on your "H:" drive will expedite your accessing the volume in the future. Do this by holding down the "Option" and the "Command(Apple)" at the same time and dragging the icon for your username_X volume over the icon for your "H:" drive. When you open your "H:" drive you should see and icon for your username_X volume; double-clicking on this icon should prompt you for you password and mount and open your username_X volume. This icon will only work from a Mac, but there is an alternative method that will work from Windows.

From a PC (Windows XP)

Open the “Map a Network Drive” dialogue box.
Select a drive letter. (I suggest “X”, since the server is an Xserve server.)
Enter “\\chemserver.chem.uwec.edu\username_X” in the Share field, where username is your university username. You will not need to enter a username and password, since the server uses your University username and password. There is a checkbox you can check if, in the future, you want the share to mount automatically when you log onto a compus PC computer.
Click the “Finish” button
Your username_X share should appear in the left-hand panel of the Windows Explorer window.

Molecular Visualization: PDB Files and Jmol

Assignment

Read Chapter 11: Tools for Studying Macromolecules in [Crystal]
Protein Data Bank
- The Protein Data Bank is a database in which each record contains the 3-dimensionial (x,y,z) coordinates of the atoms in biological macromolecules. Despite the name of the database, records are not limited to just proteins; the database also contains records for nucleic acids and nucleoproteins such as virus particles.
Go to the Protein Data Bank (PDB) site and answer the following questions (in red). Copy these questions to a Word document. Create a folder named "username_lab1" in a folder named "Chem406_Labs", which you should created on your "username_X" share. Save the Word document as "username_lab1.doc" in the "username_lab1" folder.

As of today (9/6/06), how many entries are there in the Protein Data Bank?

What is this month's "Molecule(s) of the Month"?

How many structures are there for the Pyruvate Kinase (use the Enzyme Commission (E.C.) number to search for entries)?

Download the complete pdb file for the pyruvate structure having the PDB ID of 1LIU and copy to your "username_lab1" folder.

Open the 1LIU.pdb file using BBEdit Lite. Read the header section of the pdb file.
What is the citation for the article in which this structure was reported?

Obtain a copy of this article in pdf format and save copy it to your username_lab1 folder.

How many copies of the pyruvate kinase molelcule are present in the structure?

What organic ligands (non protein molecules) are bound to the pyruvate kinase in the 1LIU structure?

What role do each of these ligands play for pyruvate kinase?

What is the reaction equation for the reaction catalyzed by Pyruvate Kinase?

What metabolic pathway is Pyruvate Kinase found in?

Create this image
- Open the 1LIU.pdb file you downloaded with the standalone version of Jmol (Jmol.jar)
- Open the Rasmol script console:

$ restrict *:a (look at only the a subunit)
$ center *:a
$ cartoon on (render the protein as a cartoon)
$ color structure (color by secondary structure)
$ select [FBP]580 (select the fructose 1,6-bisphosphate ligand)
$ spacefill on (represent with vander Waals spheres)
$ color cpk (color by element)
$ select [PGA]581 (select the phosphglycolate ligand)
$ spacefill on
$ color cpk
$ background white

Export the image as a jpeg file, name it 1LIU.jpg and save it in you username_lab1 folder
Archive your username_lab1 folder and send me the resulting username_lab1.zip file to me as an email attachment before next Wednesday.

[Chemistry Dept.] [Chem 406]

Warren Gallagher
Department of Chemistry
(715) 836-5388
wgallagh@uwec.edu

updated: Wednesday, September 6, 2006